Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS.

Joao A Paulo, Linda S Lee, Bechien Wu, Kathryn Repas, Peter A Banks, Darwin L Conwell, Hanno Steen

Department of Pathology, Children's Hospital Boston, Boston, MA, USA.

Proteomics. Clinical applications 2010 Sep

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Proteomic analysis of gastroduodenal fluid offers an alternative strategy to study diseases, such as peptic ulcer disease and gastric cancer. We use in-gel tryptic digestion followed by LC-MS/MS (GeLC-MS/MS) to profile the proteome of gastroduodenal fluid collected during the endoscopic pancreatic function test (ePFT). Gastroduodenal fluid specimens collected during ePFT from six patients with upper abdominal pain were subjected to proteomic analysis. We extracted proteins using three chemical precipitation reagents (acetone, ethanol, and trichloroacetic acid) and analyzed each sample by SDS-PAGE and GeLC-MS/MS for protein identification. Cellular origin and molecular function of the identified proteins were determined via gene ontology analysis. All three precipitation techniques successfully extracted protein from gastroduodenal fluid, with acetone resulting in excellent resolution and minimal protein degradation compared with the other methods. A total of 134 unique proteins were found in our GeLC-MS/MS analysis of ePFT-collected gastroduodenal fluid samples. Sixty-seven proteins were identified in at least two of the three samples. Gene ontology analysis classified these proteins mainly as being peptidases and localized extracellularly. ePFT, followed by acetone precipitation, and coupled with LC-MS/MS, can be used to safely collect gastroduodenal fluid from the upper gastrointestinal tract for MS-based proteomic analysis. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Citation

Joao A Paulo, Linda S Lee, Bechien Wu, Kathryn Repas, Peter A Banks, Darwin L Conwell, Hanno Steen. Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS. Proteomics. Clinical applications. 2010 Sep;4(8-9):715-25